Merge branch 'main' into feat/add_openmm_8_beta_test

choderalab · Nov 16, 2023 · 516e925 · 516e925
2 parents c427fa5 + 0bbef98
commit 516e925
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -13,74 +13,79 @@ on:
     #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
     - cron: "0 0 * * *"
 
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
 jobs:
   test:
-    name: Test on ${{ matrix.cfg.os }}, Python ${{ matrix.cfg.python-version }}, OpenMM ${{ matrix.cfg.openmm }}
-    runs-on: ${{ matrix.cfg.os }}
+    name: ${{ matrix.os }}, py-${{ matrix.python-version }}, OpenMM-${{ matrix.openmm }}, pymbar-${{ matrix.pymbar-version }}
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         cfg:
-          - { os: macOS-latest,   python-version: '3.8', openmm: latest  }
-          - { os: windows-latest, python-version: '3.8.10', openmm: latest  }
-          - { os: ubuntu-latest,  python-version: '3.8', openmm: latest  }
-          - { os: ubuntu-latest,  python-version: '3.9', openmm: latest  }
-          - { os: ubuntu-latest,  python-version: '3.8', openmm: nightly }
-          - { os: ubuntu-latest,  python-version: '3.10', openmm: latest  }
-          - { os: ubuntu-latest,  python-version: '3.8', openmm: beta  }
-          - { os: ubuntu-latest,  python-version: '3.9', openmm: beta  }
+          - { os: macOS-latest,   python-version: '3.8', openmm: dev  }
+          - { os: windows-latest, python-version: '3.8.10', openmm: dev  }
+          - { os: ubuntu-latest,  python-version: '3.9', openmm: dev  }
+          - { os: ubuntu-latest,  python-version: '3.10', openmm: dev  }
 
     env:
       OPENMM: ${{ matrix.cfg.openmm }}
+        python-version: ["3.9", "3.10"]
+        openmm: ["7.7", "8.0"]
+        os: [macOS-latest, ubuntu-latest]
+        pymbar-version: ["4"]
+        include:
+          # Test openmm dev build on newest python + linux
+          - openmm: "dev"
+            python-version: "3.10"
+            os: ubuntu-latest
+            pymbar-version: "4"
+          # Have one job test pymbar 3 support
+          - openmm: "dev"
+            python-version: "3.10"
+            os: ubuntu-latest
+            pymbar-version: "3"
 
     steps:
-      - uses: actions/checkout@v1
-
+      - uses: actions/checkout@v3
       - name: Additional info about the build
         shell: bash
         run: |
           uname -a
           df -h
           ulimit -a
 
-      # More info on options: https://github.com/conda-incubator/setup-miniconda
-      - uses: conda-incubator/setup-miniconda@v2
+      - name: Setup micromamba for openmm dev
+        uses: mamba-org/provision-with-micromamba@main
+        if: ${{ matrix.openmm == 'dev' }}
         with:
-          python-version: ${{ matrix.cfg.python-version }}
+          channels: jaimergp/label/unsupported-cudatoolkit-shim,conda-forge/label/openmm_rc,conda-forge
           environment-file: devtools/conda-envs/test_env.yaml
-          channels: conda-forge,defaults
-          activate-environment: test
-          auto-update-conda: true
-          auto-activate-base: false
-          show-channel-urls: true
-
-      - name: Install OpenMM nightly
-        shell: bash -l {0}
-        if: matrix.cfg.openmm == 'nightly'
-        run: |
-          conda install --yes -c omnia-dev openmm
-
-      - name: Install OpenMM beta
-        shell: bash -l {0}
-        if: matrix.cfg.openmm == 'beta'
-        run: |
-          conda install -c conda-forge/label/openmm_rc -c conda-forge openmm
-
+          channel-priority: flexible
+          environment-name: openmmtools-test
+          extra-specs: |
+            python==${{ matrix.python-version }}
+            openmm==8.1
+            pymbar==${{ matrix.pymbar-version }}.*
+            
       - name: Install package
         shell: bash -l {0}
         run: |
           python -m pip install . --no-deps
-          conda list
+          micromamba list
+          micromamba info
 
       - name: Run tests
         shell: bash -l {0}
         run: |
           # pytest -v --cov=openmmtools --cov-report=xml --color=yes openmmtools/tests/
-          nosetests openmmtools/tests --nocapture --verbosity=2 --with-timer --with-doctest -a '!slow'
+          nosetests openmmtools/tests --nocapture --cover-tests --with-coverage --cover-package=openmmtools --cover-xml --cover-xml-file=coverage.xml --verbosity=2 --with-timer --with-doctest -a '!slow'
 
       - name: CodeCov
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v3
         with:
           file: ./coverage.xml
           flags: unittests
-          name: codecov-${{ matrix.cfg.os }}-py${{ matrix.cfg.python-version }}
+          name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}-openmm-${{ matrix.openmm }}
diff --git a/.github/workflows/self-hosted-gpu-test.yml b/.github/workflows/self-hosted-gpu-test.yml
@@ -11,7 +11,7 @@ on:
 jobs:
   start-runner:
     name: Start self-hosted EC2 runner
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     outputs:
       label: ${{ steps.start-ec2-runner.outputs.label }}
       ec2-instance-id: ${{ steps.start-ec2-runner.outputs.ec2-instance-id }}
@@ -28,10 +28,10 @@ jobs:
         with:
           mode: start
           github-token: ${{ secrets.GH_PERSONAL_ACCESS_TOKEN }}
-          ec2-image-id: ami-096d499d418f88d88
-          ec2-instance-type: p2.xlarge
-          subnet-id: subnet-0e82552b8c708a999
-          security-group-id: sg-0589e74ec03965add
+          ec2-image-id: ami-04d16a12bbc76ff0b
+          ec2-instance-type: g4dn.xlarge
+          subnet-id: subnet-0dee8543e12afe0cd # us-east-1a
+          security-group-id: sg-0f9809618550edb98
           # iam-role-name: self-hosted-runner # optional, requires additional permissions
           aws-resource-tags: > # optional, requires additional permissions
             [
@@ -46,6 +46,8 @@ jobs:
       TEST_MODE: GPU
       OPENMM: ${{ matrix.cfg.openmm }}
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
+      HOME: /home/ec2-user
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
     defaults:
       run:
@@ -55,7 +57,7 @@ jobs:
       - uses: conda-incubator/setup-miniconda@v2
         with:
           installer-url: https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
-          python-version: 3.8
+          python-version: "3.10"
           activate-environment: test
           channels: conda-forge,defaults
           environment-file: devtools/conda-envs/test_env.yaml
@@ -66,7 +68,7 @@ jobs:
       - name: Refine test env
         shell: bash -l {0}
         run: |
-          mamba install -y cudatoolkit==11.0.3 openmm==7.7
+          mamba install -y cudatoolkit==11.7 openmm>=8.0
       
       - name: Additional info about the build
         shell: bash -l {0}
@@ -93,7 +95,7 @@ jobs:
       - name: Test the package
         shell: bash -l {0}
         run: |
-          nosetests openmmtools/tests --nocapture --verbosity=2 --with-timer --with-doctest
+          pytest -v --cov-report xml --durations=0 --cov=openmmtools openmmtools/tests 
 
       - name: Codecov
         if: ${{ github.repository == 'choderalab/openmmtools'
@@ -103,7 +105,7 @@ jobs:
           file: ./coverage.xml
           name: codecov-${{ matrix.cfg.os }}-py${{ matrix.cfg.python-version }}
           flags: unittests
-          fail_ci_if_error: true
+          fail_ci_if_error: false
 
   stop-runner:
     name: Stop self-hosted EC2 runner

diff --git a/.gitignore b/.gitignore
@@ -100,3 +100,6 @@ ENV/
 
 # mypy
 .mypy_cache/
+
+# macOS
+.DS_Store
diff --git a/README.md b/README.md
@@ -3,6 +3,7 @@
 [![Downloads Badge](https://anaconda.org/omnia/openmmtools/badges/downloads.svg)](https://anaconda.org/omnia/openmmtools/files)
 [![Documentation Status](https://readthedocs.org/projects/openmmtools/badge/?version=latest)](https://openmmtools.readthedocs.io/en/latest/?badge=latest)
 [![Zenodo DOI Badge](https://zenodo.org/badge/25416166.svg)](https://zenodo.org/badge/latestdoi/25416166)
+[![codecov](https://codecov.io/gh/choderalab/openmmtools/branch/main/graph/badge.svg?token=aGwEahm2CY)](https://codecov.io/gh/choderalab/openmmtools)
 
 ## OpenMMTools
 
@@ -45,4 +46,4 @@ Major contributors include:
 * [Iván Pulido](https://github.com/ijpulidos)
 * [Ivy Zhang](https://github.com/zhang-ivy)
 * [Dominic Rufa](https://github.com/dominicrufa)
-* [Mike Henry](https://github.com/mikemhenry)
+* [Mike Henry](https://github.com/mikemhenry)
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -1,21 +1,20 @@
-name: test
+name: openmmtools-test
 channels:
   - conda-forge
-  - defaults
-  - omnia
 dependencies:
     # Base depends
   - cython
+  - hdf5 <=1.14.0  # Macos has problem with newer releases (1.14.x) to date
   - libnetcdf >=4.6.2 # workaround for libssl issues
   - mdtraj
   - mpiplus
   - netcdf4 >=1.4.2 # after bugfix: "always return masked array by default, even if there are no masked values"
   - numba
   - numpy
-  - openmm >=7.5.0
+  - openmm
   #- parmed  # Test to see if this fixes the docs
   - pip
-  - pymbar <4
+  - pymbar
   - python
   - python
   - pyyaml
@@ -28,8 +27,9 @@ dependencies:
   - nose-timer
   - pytest
   - pytest-cov
+  - coverage
 
   # docs
   - numpydoc
   - sphinxcontrib-bibtex
-
+  - sphinx-rtd-theme
diff --git a/devtools/conda-recipe/README.md b/devtools/conda-recipe/README.md
diff --git a/devtools/conda-recipe/bld.bat b/devtools/conda-recipe/bld.bat
diff --git a/devtools/conda-recipe/build.sh b/devtools/conda-recipe/build.sh
diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml
diff --git a/devtools/conda-recipe/run_test.bat b/devtools/conda-recipe/run_test.bat
diff --git a/devtools/conda-recipe/run_test.sh b/devtools/conda-recipe/run_test.sh
-Original file line number
+Diff line change
@@ Expand Up / @@ -100,3 +100,6 @@ ENV/ @@
     # mypy
     .mypy_cache/
+    # macOS
+    .DS_Store